Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• The diploid genome sequence of an Asian individual.

  PMID 18987735 · PMC2716080 · Nature · 2008 · 8 claims · 8 setups

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  First diploid genome sequence of an Asian (Han Chinese) individual generated using massively parallel Illumina sequencing

  han donor genome genomic whole-genome g-banded snp

• Polymorphix: a sequence polymorphism database.

  PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.

  eukaryotic clustered consensus aligned sequence blast phylogenetic

• Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

  PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

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  Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

  animals cdk encephalitozoon pfmrk comparative bayesian distance

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• Comprehensive splice-site analysis using comparative genomics.

  PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

  refseq u2-type genes comparative information phylogenetic

• Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

  PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

  random trans-acting tpo fibronectin minigene selex cdna

• TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

  PMID 17986453 · PMC2238949 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  TranspoGene catalogs TEs within protein-coding genes of seven species (human, mouse, chicken, zebrafish, fruit fly, nematode, sea squirt), classified as proximal promoter, exonized, exonic, or intronic TEs.

  chicken normal tes genes genomic exon microrna

• Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

  PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

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  MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

  mip diagnostic is900-specific pgg

• Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

  PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

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  Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

  pbmc his-tagged cem mammalian pcr electrophoretic western

• Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

  PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

  redundant mammalian genomic vertebrates blast pattern-hit tblastn

• Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

  PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

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  MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

  genomic lr-pcr uhts v-4 long-range ultra sanger

• Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

  PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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  Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

  c57bl orthologous alpha-defensin defensin manual comparative sequence

• Genetic variation in PARL influences mitochondrial content.

  PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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  PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

  genomic nuclear parl pcr snp real-time

• Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

  PMID 15234325 · PMC7129141 · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2004 · 7 claims · 3 setups

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  Human aminopeptidase N (APN/CD13/ANPEP) is the receptor for human coronavirus 229E (HCoV-229E)

  genomic cloned consensus pcr molecular sequence

• Cryptosporidium: genomic and biochemical features.

  PMID 19187778 · PMC2819285 · Experimental parasitology · 2010 · 8 claims · 8 setups

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  C. parvum lacks a plastid and mitochondrial genome, unlike other apicomplexans, limiting plastid-targeted drug strategies

  parvum yeast recombinant gp40 pulsed-field happy genome

• Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

  PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

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  Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

  genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct

• Mutation analysis of the AATF gene in breast cancer families.

  PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

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  No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

  genomic showing aatf case conformation direct pathogenicity

• Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

  PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups

  Has reproduction · 67

  Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies

  frugiperda satellite million contigs comparative homology divergence

• A third approach to gene prediction suggests thousands of additional human transcribed regions.

  PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

  genome 4.4-mb known nucleotide repeat polyadenylation